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The AAP recommends using the procedure to treat a specific infection only, and only in medical centers with experience in fecal microbiota transplantation. 

The American Academy of Pediatrics provides guidance for pediatricians on the use of fecal microbiota transplantation in children within a new clinical report that looks at the promising uses of the procedure and what remains unknown. Fecal microbiota transplantation has been successful in treating a potentially life-threatening infection, Clostridioides difficile. 

The clinical report, “Guidance for the Clinician in Rendering Patient Care Fecal Microbiota Transplantation: Information for the Pediatrician,” is published in the December 2023 issue of Pediatrics (published online Nov. 20).  The report, written by the Section on Gastroenterology, Hepatology and Nutrition and Committee on  Infectious Diseases, recommends the use of fecal microbiota transplantation in children with a moderate to severe or a recurrent infection of Clostridioides difficile, also called CDI or C-diff.  

“Many things can disrupt the microbial ecosystem in our gut, including the antibiotics we sometimes take for bacterial infections,” said Maria Oliva-Hemker, MD, FAAP, lead author of the report. “Children can also pick up this infection in the community. This infection can cause serious issues for children, especially those who have chronic health conditions.” 

Fecal microbiota transplantation involves the transfer of stool from a healthy donor to another individual, to replace “good” bacteria in the gut that has sometimes been destroyed by use of antibiotics. 

In adults, the fecal transplantation method has an approximately 80-90% cure rate for Clostridiodes difficile infection, and some research finds similar results for children. This success has led to increasing interest in fecal transplantation as a therapeutic intervention for other conditions associated with disturbances of the intestinal microbiome, including inflammatory bowel diseases, autism spectrum disorder, and obesity. 

Yet evidence for its use in treating other conditions is inconclusive and lacking in children.

The AAP does not recommend the treatment for any other medical conditions in children at this time and strongly discourages do-it-yourself transplants at home for safety reasons.  

Other conclusions:

  • Fecal microbiota transplantation should always  be performed in a center with experience in the procedure. .
  • There is a lack of regulatory standards for fecal preparations used in this treatment.
  • The long-term effects of fecal microbiota transplantation are unknown.  
  • The field of microbial therapies is anticipated to quickly advance. 

This clinical report endorses the joint society statement by the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition and the European  Society for Pediatric Gastroenterology, Hepatology and Nutrition. 


The American Academy of Pediatrics is an organization of 67,000 primary care pediatricians, pediatric medical subspecialists and pediatric surgical specialists dedicated to the health, safety and well-being of infants, children, adolescents and young adults.

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